If you cut or move an audio clip, (that has an envelope on it), it will sometimes mess with the envelopes.
 
HTH

I have also found that when you have "select envelopes with clips" selected, strange things sometimes happen when you drag out a copy of a clip. For instance: 
 

When I drag-copy the clips over, what should happen is that the automation is copied over with them, and the automation under the original clips stays intact. But as you can see, it has destroyed the original automation and placed a seemingly random node in its place. Of course I couldn't reproduce this in a fresh project, it's just one of those weird unpredictable glitches that frustrates me almost every time I work on a project. I spend half my time dealing with nonsense like this when I should be exercising my creativity. 

I'm not moving or cutting anything. When I record new automation, sometimes older automation envelopes/nodes disappear earlier on the timeline in the same or different tracks. It seems quite random. I tried deselecting everything, dis-arming and re-arming automation, etc. I can detect no consistent pattern to reproduce.
 
Is there perhaps a buffer setting somewhere that can be increased, changed, etc.?